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Discovered to have mathematical abilities at age 3, his parents put his education first, ahead of almost everything else. Giving him private tutors and helping him advance rapidly through school. He graduated High school on the same day as his older brother Don, much to his older brothers resentment. Through out high school, not much is known about what happened between the brothers, except that they did fight over Val Eng, who was Charlie's lab partner and first crush, unbeknown to his brother who took her to prom.
He went to Princeton at the age of 13 with his mother who felt he was to young to travel so far on his own. After graduating from Princeton he went to Europe to study abroad on his own to further his career. While there he meet Susan Berry with whom he lived for about 2 years. After receiving his degrees, he returned to Los Angeles and became a professor at CalSci. He teamed up with long time mentor and friend Larry Fleinhart, whom Charlie first met at Princeton.
About a year prior to the start of the show Margret Eppes, Charlie's mother, succumbed to cancer. Charlie was unable to handle her diagnosis and subsequent death. Three months prior to her death he locked himself in the garage to work on a world famous unsolvable math problem called P vs NP. It is believed that he set out to work on it with the belief that if he could solve it he could cure his mother's cancer. Due to the nature of the problem, this is unlikely. His actions during his mother's illness put a strain on his relationship with his brother that would take years to rectify.
Although not yet 30 he was a tenured professor at CalSci.

Charlie began to help his brother in various cases, to the dazzle of Don and his team. With the help of Larry Fleinhardt and a young woman named Amita Ramanujan, Charlie would solve crimes using his math skills. He became a common sight around the FBI office. During the LA Sniper Zero Case he became a deadly sniper's target, though he came out unscathed.

Charlie had been living with his father for most of his time in LA; however, his father had decided to sell the Eppes home. Charlie, unable to convince his dad otherwise, bought the house, not wanting to let go of the home.

As a romantic relationship between Charlie and Amita began to flower, they found that they had trouble communicating outside of work. Charlie got the first kiss from Amita in S02E14 when Charlie suggested Amita to go and meet her grand mother about advise.